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Re: [Psidev-ms-dev] PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT
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From: Trish W. <wh...@pc...> - 2007-04-17 04:02:35
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Hi Pete, Thanks for the clarification. All sounds good, just trying to keep track of things. Trish > I have not added new terms. These are the terms which you pulled out from > tiny1.DataXML0.11.filerev11.dataXML.xml and tiny1.mzData1.05.xml instance > docs. I realized that some terms needed discussion while other could be added > to 1.7.4 obo file. There were also terms whose definitions needs to be > updated and then there are terms from the instance docs that we decided not > to add. I basically summarized the discussions we were having in emails about > these terms. > It contains many of the terms that needed definitions, mostly mass spec > models and TODO terms that you had in 1.7.4 obo file. All the terms and > issues that were under in discussionItemsAboutCV.txt are covered in > PSI_TermsReview_Merge.txt. > > Let me know if there is confusion or something that I missed. I just broke > them into categories: > > Terms that need debate:, Terms to be added:, Terms whose definitions needs > to be updated: and Terms we decided not to add: > > Pete. > > > Let me know > > > Trish Whetzel wrote: >> Hi Pete, >> >> Did you add terms to the OBO file? I did not see any new terms added to the >> tracker. >> >> Is the list attached here a further review of the terms that I sent >> questions on or are there new terms included in this list? At first glance, >> I am not sure how this list relates to the list that I sent to you and >> Eric. >> >> Thanks, >> Trish >> >> >> >>> Hi everyone, this is a reminder of the conference call Tuesday, 9am PDT, >>> 12n EDT, 4pm GMT. Agenda items are: >>> >>> - Review recent work on the CV (see attached list of items to discuss >>> from Pete) >>> - Discuss required preparation for next week >>> <<PSI_TermsReview_Merge.txt>> >>> MS-WG ccall Tuesday, 9am PDT, 12n EDT, 4pm GMT >>> >>> - Phone numbers: >>> + Germany: 08001012079 >>> + Switzerland: 0800000860 >>> + UK: 08081095644 >>> + USA: 1-866-314-3683 >>> + Generic international: +44 2083222500 (UK number) >>> >>> access code: 297427 >>> >>> Thanks, >>> Eric >>> >>> >>> _____________________________________________ >>> From: Eric Deutsch >>> Sent: Monday, April 09, 2007 1:07 AM >>> To: 'Pierre-Alain Binz'; Trish Whetzel; Puneet Souda; Kent Laursen; >>> psi...@li... >>> Cc: Eric Deutsch >>> Subject: PSI-MS WG ccall Tue 9am PDT, 12n EDT, 4pm GMT >>> >>> Hi everyone, here is a summary of the issues before us regarding >>> dataXML. Please read it over and let's discuss at the conference call >>> on Tuesday. Call information: >>> >>> MS-WG ccall Tuesday, 9am PDT, 12n EDT, 4pm GMT >>> >>> - Phone numbers: >>> + Germany: 08001012079 >>> + Switzerland: 0800000860 >>> + UK: 08081095644 >>> + USA: 18663143683 >>> + Generic international: +44 2083222500 (UK number) >>> >>> access code: 297427 >>> >>> ------------------------------------------------------------------------ >>> -------------------------- >>> >>> Open issues with dataXML >>> >>> - Need documentation of each element and attribute >>> Mike Coleman 2007-02-06 >>> Agreed. Does Kent have some start of documentation from >>> current/previous XMLSpy docs? >>> >>> Eric will contact Kent directly >>> >>> - Need more specifics on the desired numerical formats (e.g., IEEE, >>> etc.) >>> Mike Coleman 2007-02-06 >>> To be discussed in Lyon >>> >>> - Should there be "count" attributes? >>> Frederik Levander 2007-02-06 >>> This is useful for some parsers. Probably leave in place. Discuss in >>> Lyon >>> >>> - Should file index be within the file or in a separate file? >>> Frederik Levander 2007-02-06 >>> The implementation of dataXML to be presented at Lyon will include >>> this information in the same file. Further discussion deferred to the >>> Lyon meeting The question was there: Should the file name / checksum >>> information be held in a separate file? >>> >>> - Encoded filename should be element content instead of an attribute, so >>> that CDATA could be used >>> Alex Masselot 2007-02-07 >>> To be discussed in Lyon >>> >>> - Should controlled vocabulary term values also be element content >>> instead of attribute so that CDATA could be used? >>> Alex Masselot 2007-02-07 >>> To be discussed in Lyon >>> >>> - How will we handle multiple charges for parent peak, and fragmentation >>> peaks? >>> Alex Masselot 2007-02-07 >>> This is already handled - mutliple cvParams of the same type can be >>> used to annotate one peak / spectrum. >>> >>> - How can we allow two cv terms to be linked, such as concept with value >>> and the associated units (a separate cv term). (e.g. "collision >>> energy"=35.0 & "energy units"="joules") >>> Phil Jones 2007-02-27 (followup by Angel and Kent 02-28) >>> Phil to post to list for further responses >>> >>> Phil suggested 2 possibilities: <annotation> and additional attributes >>> Angel suggested doing the FuGE way. Maybe overkill? Difficult for >>> software to handle? >>> Do we really need having both or could we encode the units within the >>> terms, e.g. "collision energy in joules" >>> Most other relevant CVs don't seem to encode units as part of the term >>> Defer this to Lyon? Try to include the CV folks in a conference call >>> during meeting >>> Do we need to have specific types of relationships between linked terms, >>> like "has_units"? >>> >>> - People still wrinkle their nose when hearing the "dataXML" name. We >>> have a suggestion on the floor to rename to "mzDataXML". Comments? >>> >>> - Make sure dataXML web site is up to date as can be >>> >>> - DONE Add link to XMLSpy-generated documentation at: >>> >>> http://gelbank.anl.gov/schema/documentations/dataXML0.11/dataXML0.11.htm >>> l >>> >>> - Get the indexing wrapper schema working properly >>> Jayson Falkner 2006-11-15 >>> >>> - Make sure that Karl Klauser is invited to be involved >>> >>> Eric will send email. >>> >>> - Do we support properly the spectrum "library" use case? >>> Karl Klauser 2007-01-18 >>> dataXML is supposed to be for MS instrument raw data, not interpreted >>> data, i.e. with assignments. That is what analysisXML is intended for. >>> >>> Still open questions here. If analysisXML doesn't includes spectra, this >>> would be tricky. >>> >>> - Examine the mapping with MIAPE. Do we support everything MIAPE >>> requires? >>> Pierre-Alain Binz 2007-03-30 >>> This will be addressed in Lyon >>> >>> - Revisit the chromatogram use case and develop a good example >>> >>> >>> Controlled Vocabulary Issues: >>> >>> Trish sent out a new version of the CV this morning. >>> New terms from Dave Horn added >>> Will start keeping and posting release notes >>> Pete should start working on this new version now >>> Pete, Trish, and I will iterate on CV a little and there will be another >>> ccall in 1 week exactly to discuss further >>> We should post the OBO file soon on OBO. >>> >>> We will meet again in a week roughly, but Pete can't do next Tue 9am >>> >>> - DONE. Add hyperlink to the current CV on the web site >>> http://psidev.sourceforge.net/ms/xml/mzdata/psi-ms-cv-latest.obo >>> >>> - Should we change the ontology namespace to PSI-MS? >>> Trish Whetzel 2007-03-27 >>> Was suggested in Washington already and we decided no? >>> >>> - What is the overlap/division between the PSI-MS CV, the main PSI CV, >>> OBI? >>> Trish Whetzel, Luisa Montecchi 2007-03-30 >>> To be sorted out in a special working session in Lyon? >>> >>> - Should we even have an InstrumentIdentifier (local to lab) term at >>> all? >>> Trish Whetzel 2007-03-19 >>> >>> - What is required from vendors? >>> Pierre-Alain 2007-04-03 >>> >>> - How do we deal with the common PSI CV? >>> Pierre-Alain 2007-04-03 >>> >>> - What is the overlap with OBO ontology "ProPreo"? >>> ProPreo: A comprehensive proteomics data and process provenance >>> ontology >>> http://lsdis.cs.uga.edu/projects/glycomics/propreo/ >>> Eric Deutsch 2007-04-03 >>> >>> Trish says there was a quick review of this ~ 8 months ago >>> ProPreo is broader but not deep enough >>> >>> - Try to reconcile the latest instance document and the current PSI >>> ontology: >>> Trish Whetzel 2007-03-30 >>> Eric Deutsch responded 2007-04-03 >>> (full exchange not repro'ed here) >>> Pete or someone trying to resolve based on discussion thus far and >>> identify unresolved? >>> >>> >>> >>> >>> >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by DB2 Express >> Download DB2 Express C - the FREE version of DB2 express and take >> control of your XML. No limits. Just data. Click to get it now. >> http://sourceforge.net/powerbar/db2/ >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> |
